Background: Immunotherapy combinations including ipilimumab and nivolumab are now the standard of care for untreated metastatic renal cell carcinoma (mRCC). Biomarkers of response are lacking to predict patients who will have a favorable or unfavorable response to immunotherapy. This study aimed to use the OmniSeq transcriptome-based platform to develop biomarkers of response to immunotherapy., Methods: Two cohorts of patients were retrospectively collected. These included an investigational cohort of patients with mRCC treated with immune checkpoint inhibitor therapy from five institutions, and a subsequent validation cohort of patients with mRCC treated with combination ipilimumab and nivolumab from two institutions (Duke Cancer Institute and Cleveland Clinic Taussig Cancer Center). Tissue-based RNA sequencing was performed using the OmniSeq Immune Report Card on banked specimens to identify gene signatures and immune checkpoints associated with differential clinical outcomes. A 5-gene expression panel was developed based on the investigational cohort and was subsequently evaluated in the validation cohort. Clinical outcomes including progression-free survival (PFS) and overall survival (OS) were extracted by retrospective chart review. Objective response rate (ORR) was assessed by Response Evaluation Criteria in Solid Tumors (RECIST) V.1.1., Results: The initial investigation cohort identified 86 patients with mRCC who received nivolumab (80%, 69/86), ipilimumab/nivolumab (14%, 12/86), or pembrolizumab (6%, 5/86). A gene expression score was created using the top five genes found in responders versus non-responders (FOXP3, CCR4, KLRK1, ITK, TIGIT). The ORR in patients with high gene expression (GE high ) on the 5-gene panel was 29% (14/48), compared with low gene expression (GE low ) 3% (1/38, χ 2 p=0.001). The validation cohort was comprised of 62 patients who received ipilimumab/nivolumab. There was no difference between GE high and GE low in terms of ORR (44% vs 38.5%), PFS (HR 1.5, 95% CI 0.58 to 3.89), or OS (HR 0.96, 95% CI 0.51 to 1.83). Similarly, no differences in ORR, PFS or OS were observed when patients were stratified by tumor mutational burden (high=top 20%), PD-L1 (programmed death-ligand 1) expression by immunohistochemistry or RNA expression, or CTLA-4 (cytotoxic T-lymphocytes-associated protein 4) RNA expression. The International Metastatic RCC Database Consortium (IMDC) risk score was prognostic for OS but not PFS., Conclusion: A 5-gene panel that was associated with improved ORR in a predominantly nivolumab monotherapy population of patients with mRCC was not predictive for radiographic response, PFS, or OS among patients with mRCC treated with ipilimumab and nivolumab., Competing Interests: Competing interests: LCB declares the following relationships: Consulting with Seattle Genetics. JZ declares the following relationships: Consulting with Tempus. KD declares the following relationship: Consulting with Tyra BioSciences. EK declares that she has no conflicts of interest that might be relevant to the contents of this manuscript. CK declares that he has no conflicts of interest that might be relevant to the contents of this manuscript. YHL is/was an employee at OmniSeq. SP is/was an employee at OmniSeq. MKL declares that he has no conflicts of interest that might be relevant to the contents of this manuscript. JT declares that she has no conflicts of interest that might be relevant to the contents of this manuscript. KHD declares that he has no conflicts of interest that might be relevant to the contents of this manuscript. LJT declares that she has no conflicts of interest that might be relevant to the contents of this manuscript. FD declares that he has received research grants (to the institution) from AstraZeneca, Bristol Myers Squibb, Merck, Genentech/Roche, Taiho, Exelixis, Trishula, Leap Therapeutics, has received a speaker honorarium from Amgen, Eisai, Ipsen, Exelixis, Sirtex, Deciphera, Ipsen, Natera, and has received a consultancy honorarium from Natera, QED, Eisai, Exelixis, Genentech/Roche. RTG declares the following relationships: Bayer Pharma AG—consultant & speakers bureau, Invivo—consultant, Bard—consultant, DxTx Medical—consultant, Quibim—consultant, Bracco Diagnostics—consultant. SM declares the following relationships: AstraZeneca—consultant; Takeda Pharmaceuticals—speaker, honorarium. DJG declares the following relationships: Acerta Pharmaceuticals—research; American Association for Cancer Research—senior editor; Astellas—consultant, research, advisory board; AstraZeneca—consultant, advisory board; Axess Oncology—independent contractor; Bayer H/C Pharmaceuticals—research, consultant, speaker, honorarium, travel accommodations; SC, BMS—consultant, research, steering committee; Calithera—research; Capio Biosciences—scientific advisory board; EMD Serono—honorarium; Exelixis—research, consultant, speaker, honorarium, travel accommodations; Flatiron—consultant; Ipsen—honorarium; Janssen Pharmaceuticals—research, consultant, Independent Data Monitoring Committee; Leidos Biomedical Research—consultant; Merck Sharp & Dohme—consultant; Michael J Hennessey Associates—honorarium, consultant; Millennium Medical Publishing, Clinical Advances in Hematology & Oncology—co-editor-in-chief; Modra Pharmaceuticals B.V.—advisory board; Myovant Sciences—consultant; Nektar Therapeutics—steering committee; Novartis—research; Physician Education Resource LLC—consultant; Pfizer—research, consultant, steering committee, honorarium; Sanofi—research, consultant, speaker, honorarium, travel accommodations; UroGPO—honorarium; UroToday—honorarium, travel accommodations; Vizuri Health Sciences, LLC—consultant; NCI—steering committee. YHL is/was an employee at OmniSeq. STG is/was an employee at OmniSeq. MKN is/was an employee at OmniSeq. SG declares the following relationships: Aveo—advisory board, personal, advisor/consultant; Bayer—advisory board, personal, advisor/consultant; BMS—advisory board, personal, advisor/consultant; Corvus—advisory board, personal, advisor/consultant; Eisai—advisory board, personal, advisor/consultant; EMD Serono—advisory board, personal, advisor/consultant; Exelixis—advisory board, personal, advisor/consultant; Merck—advisory board, personal, advisor/consultant; Pfizer—advisory board, personal, advisor/consultant; QED Therapeutics—advisory board, personal, advisor/consultant; Sanofi/Genzyme—advisory board, personal, advisor/consultant; Seattle Genetics—advisory board, personal, advisor/consultant; Agensys—local PI, institutional, no financial interest; Aravive—local PI, institutional, no financial interest; Aveo—local PI, institutional, no financial interest; Bayer—local PI, institutional, no financial interest; BMS—local PI, institutional, no financial interest; Calithera—local PI, institutional, no financial interest; Corvus—local PI, institutional, no financial interest; Eisai—local PI, institutional, no financial interest; Exelixis—local PI, institutional, no financial interest; Gilead—local PI, institutional, no financial interest; Merck—local PI, institutional, no financial interest; Novartis—local PI, institutional, no financial interest; Pfizer—local PI, institutional, no financial interest; Seattle Genetics—local PI, institutional, no financial interest; Surface Oncology—local PI, institutional, no financial interest. MZ declares the following relationships: Consulting or advisory roles for: Exelixis, Pfizer, Aveo, EMD Serono, Janssen, Blue Earth; Institutional research funding from Bristol Myers Squibb, Exelixis. CM is/was an employee at OmniSeq. MCO declares the following relationships: Consulting or advisory roles for Eisai, Exelixis, Pfizer, Aveo, Merck, and Bristol Myers Squibb; speakers bureaus for Bristol Myers Squibb and Exelixis; institutional research funding from Bristol Myers Squibb, Pfizer, Merck, AstraZeneca, Astellas; reimbursement for travel and accommodations expenses from Bristol Myers Squibb, Pfizer, and Exelixis. TZ declares the following relationships: Research funding (to Duke University) from Pfizer, Janssen, Acerta, AbbVie, Novartis, Merrimack, OmniSeq, PGDx, Merck, Mirati, Astellas, and Genentech; Speaking with Genomic Health and Sanofi Aventis; Consulting/Advisory board with AstraZeneca, Bayer, Pfizer, Janssen, Merck, Amgen, MJH Associates, BMS, Dendreon, Calithera, QED therapeutics, Aveo Therapeutics, Eli Lilly, SeaGen, Sanofi-Aventis, Pharmacyclics, Aptitude Health, PeerView, Clinical Care Options. Stock ownership/employment (spouse) from Capio Biosciences, Archimmune Therapeutics and Nanorobotics., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)